|
| Status |
Public on Oct 02, 2009 |
| Title |
Wild-type |
| Sample type |
RNA |
| |
|
| Source name |
total RNA from wild type animals
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2
|
| Growth protocol |
Synchronous populations of wild type and csr-1(tm892) animals were grown for 54 hours post-hatching at 20 C on OP50 E. coli at a density of approximately 50000 animals per 15cm Petri dish.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using TRI-Reagent (MRC Laboratories). Instead of pelleting and resuspending the RNA (as described in the TRI Reagent protocol), RNA was recovered, washed and eluted using the RiboPure total RNA isolation kit (Ambion).
|
| Label |
biotin
|
| Label protocol |
Reverse transcritption was performed on 7µg of each sample using the GeneChip WT Double-Stranded cDNA Synthesis Kit. The dsDNA was then purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified. 7.5µg of each dsDNA sample were used for the subsequent fragmentation and labeling reactions, using the GeneChip WT Double Stranded DNA Terminal Labeling Kit (Affymetrix).
|
| |
|
| Hybridization protocol |
Hybridization to the arrays was made using standard Affymetrix protocols and reagents
|
| Scan protocol |
Scanning was done with GeneChip Scanner 3000 7G at the University Massachusetts Medical School’s Genomics Core Facility
|
| Description |
n/a
|
| Data processing |
Signal values for each array probe were calculated using Affymetrix Tiling Analysis Software 1.1.2 (bandwidth: 30; intensities: PM/MM) with three csr-1(tm892) replicates as the experimental datasets and three wild type replicates as the controls. Probe overlap with annotations was assessed using the Affymerix-provided ce4 coordinate, which indicates the genomic position matching the center of the array probe. Only genes with signal for at least 10 different probes in either the wild type or csr-1(tm892) samples were included for analysis.
Affymetrix probe coordinates (release WS170) were converted to release WS192 coordinates using a Perl script. Gene expression values were defined as the geometric mean of all probe signals within a gene that had a P-value of <0.1. Actin was used to normalize expression values prior to comparison.
|
| |
|
| Submission date |
Sep 16, 2009 |
| Last update date |
Sep 21, 2009 |
| Contact name |
Julie M. Claycomb |
| Organization name |
University of Massachusetts Medical School
|
| Department |
Program in Molecular Medicine
|
| Lab |
Craig Mello
|
| Street address |
373 Plantation Street Biotech2 Suite 219
|
| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL5634 |
| Series (2) |
| GSE18141 |
Gene expression profile of csr-1(tm892) animals compared to wild type |
| GSE18167 |
Gene expression in csr-1 mutants and sequencing of sRNAs from CSR-1 IP complexes and csr-1 and ego-1 mutants |
|
